Classification of thermophilic actinobacteria isolated from arid desert soils, including the description of Amycolatopsis deserti sp. nov

• Published in: Antonie van Leeuwenhoek Vol. 109; no. 2; pp. 319 - 334
• Main Authors: Busarakam, Kanungnid, Brown, Ros, Bull, Alan T, Tan, Geok Yuan Annie, Zucchi, Tiago D, da Silva, Leonardo José, de Souza, Wallace Rafael, Goodfellow, Michael
• Format: Journal Article
• Language: English
• Published: Cham Springer International Publishing 01-02-2016; Springer Nature B.V
• Subjects: Actinobacteria; Actinomycetales - classification; Actinomycetales - genetics; Actinomycetales - isolation & purification; Actinomycetales - metabolism; algorithms; Amycolatopsis; Amycolatopsis methanolica; Australia; Bacteria; Biomedical and Life Sciences; chemotaxonomy; Deoxyribonucleic acid; Desert Climate; Desert soils; Deserts; DNA; DNA primers; DNA, Bacterial - genetics; DNA, Ribosomal - genetics; genes; Hot Temperature; Life Sciences; Medical Microbiology; Microbiology; Molecular Sequence Data; new species; nucleotide sequences; Original Paper; Phylogenetics; Phylogeny; Plant Sciences; ribosomal RNA; RNA, Ribosomal, 16S - genetics; Soil - chemistry; Soil Microbiology; Soil microorganisms; Soil Science & Conservation; Taxonomy; Desert soils; Polyphasic taxonomy; Amycolatopsis
• ISSN: 0003-6072; 1572-9699
• DOI: 10.1007/s10482-015-0635-8

The taxonomic position of 26 filamentous actinobacteria isolated from a hyper-arid Atacama Desert soil and 2 from an arid Australian composite soil was established using a polyphasic approach. All of the isolates gave the diagnostic amplification product using 16S rRNA oligonucleotide primers specific for the genus Amycolatopsis. Representative isolates had chemotaxonomic and morphological properties typical of members of the genus Amycolatopsis. 16S rRNA gene analyses showed that all of the isolates belong to the Amycolatopsis methanolica 16S rRNA gene clade. The Atacama Desert isolates were assigned to one or other of two recognised species, namely Amycolatopsis ruanii and Amycolatopsis thermalba, based on 16S rRNA gene sequence, DNA:DNA relatedness and phenotypic data; emended descriptions are given for these species. In contrast, the two strains from the arid Australian composite soil, isolates GY024ᵀ and GY142, formed a distinct branch at the periphery of the A. methanolica 16S rRNA phyletic line, a taxon that was supported by all of the tree-making algorithms and by a 100 % bootstrap value. These strains shared a high degree of DNA:DNA relatedness and have many phenotypic properties in common, some of which distinguished them from all of the constituent species classified in the A. methanolica 16S rRNA clade. Isolates GY024ᵀ and GY142 merit recognition as a new species within the A. methanolica group of thermophilic strains. The name proposed for the new species is Amycolatopsis deserti sp. nov.; the type strain is GY024ᵀ (=NCIMB 14972ᵀ = NRRL B-65266ᵀ).